Something Wicked Comes My Way
by PurpleMagi
Summary: The Maze trials were a success as were the Scorch trials, however the government had finally caught up with Wicked and turned out the apocalypse had not actually happened. Thomas was finally free from them however it does not mean he's not giving up one kind of hell for another, it's even harder with his memories patchy at best. Finding out he has a family is harder still.
1. Chapter 1

**So this is not going to follow fully with the books and based more on the films but I have changed it to fit with what I am doing I am going to add more people in later as well anywho enjoy.**

 **Chapter 1**

Thomas wakes up breathing in deep gulps of air into his lungs; it felt like he hadn't been able to take a deep breath for a long time. That could have been because of the maze trails and then heading out into the scorch, turned out that hadn't been real all fake. Thomas put his face in his hands breathing in deep lungful's as he let the panic wash over him, he should feel relieved that it's all over that its done but all he could sense was a deep feeling of panic that whatever he had left behind had only just begun. He was lucky that he had friends in Newt and Minho the only family that he could remember, not that he could remember a lot especially with his selective amnesia. Some days he got flashes of himself in the lab at wicked other days he would have nothing. The doctors believed that he would probably never recover his full memories so for the moment he would have to wait to find out who he once was.

The government or whoever they called themselves believed wicked picked up teenagers from the ages of 13 to 18, they had to be smart, strong, independent, leaders and resistant in their own right. They wanted them to be the next breed of soldiers trained in survival and combat, how the government never realised shocked Thomas himself.

The white rooms here in what they called a hospital reminded Thomas of the facilities that they were kept at while under wicked. He had managed in the week since being rescued to speak to Minho and Newt briefly but overall he felt like a prisoner more than ever, a performing monkey that they were waiting for him to put a show on for. A show that he would hopefully never would put on.

The door opened and a nurse in her mid-thirties walked in, she had been looking after him for around a week now since he had come in, her name was Trudy and that was all he knew about her.

"Good morning Thomas, I hope you're doing well?" she asked, he nodded along as for the past week it was the same greeting and that was the expected answer. "I need to take some more blood, hold your arm out" he did as told "Thank you, now you might feel a slight pain and then it will be over." She started humming a slight tune as she worked he watched the thick red liquid pass down the tube and into the vial. They had taken bloods every few days and to be honest he was bored. "All done" she said as she placed a plaster on his arm.

"Do you know when we are being released?" the question shocked her to be honest he hadn't been the most cooperative patient, she smiled gently at him

"I am not sure but I can find out for you, I have heard you would be moving to a different centre where it is more open" she smiled again before picking up her tray filled with his blood before leaving.

Today would be another long day bored out of his mind with nothing to do filled with staring at a blank wall. Hopping off his bed Thomas walked into the bathroom at the opposite side of the room, he looked better with the dark rings slightly fading under his whiskey coloured eyes his skin was now clean from blood and mud which made him look a bit younger. Sighing he turned away and got on with his morning ritual.

A couple of hours passed before his door opened again and a man in a black suit came in, he was slightly grey and wore a stern expression.

"Follow me Thomas, we have a few questions to ask you before you can visit the others" he said in a rather gruff voice. Jumping I got off my bed and followed him through the maze of corridors before we ended up in a lounge type room with comfy sofas and potted plants, very homely which made me a tad more nervous. The gruff man sat down in front of me and held out his hand for me to shake.

"I'm Agent Penne with the FBI" The FB what? I felt like half the time my brain supplied the information or it didn't and this was not the time, I just assumed he was with the government. "Now I need to ask you a few questions about the maze trails, can you help me Thomas I feel this could be beneficial for all."


	2. Chapter 2

**Chapter 2**

 **End of Season 3B and 2 years before current time.**

Scott sat amongst his pack at Derek's loft with Kira sitting snug next to him, he smiled as he looked around at his pack. Ever since he had turned into a true alpha he felt he had failed as the alpha but looking around him at his pack he felt for the first time since becoming alpha like a true pack. Isaac and Allison sat cuddling on the sofa she winced in pain as Isaac moved a tad from her injury, Lydia, Malia and Peter all sat in separate chairs whilst Derek was bringing in snacks before they started the pack meeting. Stiles was coming in a bit later as he was spending family time with his dad. Everyone settled down in their places chatting happily apart from Peter who Lydia was ignoring by not looking his way.

"Right. Now everyone's here, we can get this meeting started." He began as he waited for everyone to finish their conversations. "This morning Derek caught a scent in the northern edges which was confirmed to be a rouge werewolf" Derek nodded and he carried on "Did anyone see anything in the areas you scouted?"

"I asked my Dad whilst he was tracking around town and he hadn't found anything that suggested it was close to the town." Allison started, that seemed to take a lot of tension out of the group as it meant it was not taking risks attacking large groups, that didn't mean that it wouldn't attack smaller groups.

"Unlike some" muttered Lydia pointedly still not looking at Peter.

"Hey, I thought we had gotten past that and anyways I was a tad insane." Peter added pointedly. Derek just snorted at that.

"Alright enough, Isaac did you find anything?" I changed the topic before it turned into a full blown out fight after all it had happened before.

"Um, I found some foot prints but no scent however there was a dead rabbit at the western edge closer to the Hale house." That didn't sound good especially if it has decided to start killing things it was only a matter of time. He was about to ask Isaac more when the door was pulled open and the sheriff was standing in the doorway looking worried.

"Has anyone seen Stiles?" The sheriff said fear clutched my heart I looked around and everyone was shaking their heads.

"I thought he was with you"

"He was, he headed out to get some food three hours ago and hasn't returned, Scott can you use your werewolfy powers to find him I feel like somethings wrong." The sheriff looked worried deep lines on his face.

"Yes of course where was he headed" I said with a worried tone. The sheriff was about to talk when Peter beat him to it.

"I caught a scent whilst on the way here it smelt like wolf by the old oak tree." Peter said.

"Why didn't you say anything sooner if my son is dead because you forgot to inform Scott of this I will…"

"It was only half an hour ago and plus I was on the way here I didn't think it would matter." Peter retorted not looking worried in the least.

"Right we can deal with Peter after but for now let's head to the oak, Isaac I want you and Derek to scout round the edge, Kira and Lydia can keep an eye on the cars so it does not run into them and Peters with me."

"What about me?" Allison said looking a bit upset she had nothing to do.

"You can go with the sheriff and look around the roads in those areas I know you can handle yourself but you are still healing and I can't risk you after last time." Then everyone was rushing out knowing that if they didn't find the werewolf Stiles could be hurt or worse.

Half an hour later Peter and I were nearing the oak with a faint scent of feral wolf on the air.

"Well isn't this ominous" Peter chuckled as I glared at him, I may have accepted him into the pack as they say the devil you know, but I wasn't going to take bullshit from him. The oak was in front of us when a howl from Isaac came to us. We both froze as I let another howl out letting him know we both heard him. Peter and I listened as three pairs of footsteps headed towards us getting into our fighting stances as the feral werewolf let loose a roar charging at me. He was wolfed out but still had golden eyes that meant he hadn't killed an innocent that there was still a chance of saving him.

I dodged an attack as he swung his claws at me and pushed him away. He came at me again this time aiming for my face I dodged grabbing an arm before bashing him on the head he looked dazed and his eyes started flashing from gold to human blue to gold again. That was not normal, Peter stepped forward claws out and about to go for the kill.

"STOP" I shouted Peter stopped unable to refuse his alpha. The werewolf attacked again but it seemed like he didn't want to but was unable to stop. As he went for me again I grabbed his head and bashed it onto the tree as he crumpled onto the floor unconscious.

"What is wrong with you I had a clean kill then it was bye bye little wolf" Peter snarled at me his eyes flashing blue and mine flashing red in answer to the challenge.

"Guys" Isaac said "GUYS"

"WHAT" Both Peter and I said at the same time. Isaac whimpered a bit as we turned our glares on him whilst Derek rolled his eyes.

"They have found Stiles jeep" said Derek

"Where?" and we were off again to meet up with Allison and the Sheriff. We turned up to find Stiles jeep in the middle of the road still on the lights blaring out into the dark with the driver's door open but no sign of stiles and no blood, nothing it was like he had vanished into thin air.

"We need to find my son please find him" The sheriff pleaded with everyone and anyone. 24 hours later the Sheriff filed a missing person's report.

 **24 hours later in a facility.**

Stiles woke up his head pounding the last thing he remembered was being on the old oak road going back to his fathers as at the main road there had been an accident. He groaned again and sat up suddenly only to hit his head on something solid and what sounded like glass. Jerking awake fully with the pain he looked around to see he was in some sort of glass tube. Looking out he saw an older women with blond hair in a white suite.

"Hey let me out." Stiles shouts while pounding on the glass.

She smiles "You are going to do just well here Stiles"

"What do you mean, come one dude just let me out" she smiles at him again before pulling a lever.

"Just relax it will be over soon" she nods to the man behind her before she starts walking away.

"Hey wait come back" Stiles shouts something wet is soaking into his feet and then a shower of water falls on his head and starts filling up the tank. Panic fills Stiles as the water level rises. "Wait, come back come back" he screams taking a deep breath as the last of the tank fills up still bashing on the glass as he starts to become light headed from the lack of oxygen to his brain.

A voice fills the tank the same as the women before. "Just let go Stiles it will be all over soon" Finding it hard to concentrate his body releases the rest of his air bubbles as his body automatically takes in a breath and he gets lung fulls of water his eyes starting to become heavy "Just let go" the voice says before he falls into the darkness.

He wakes up with his brain fuzzy like its full of interference before he gets nothing. He sits up and an older women with blond hair pulled back in a bun looks at him and smiles warmly.

"Why can't I remember anything? Why can't I remember who I am?" he says his voice rusty as though he had been screaming. The lady gets up and walks over to him laying a warm hand on his shoulder.

"Hello I am Ava Paige but you can call me Ava." She says he looks into her blue eyes "Can you remember your name" She asks kindly. He tries he really does but all he gets is blankness he starts panicking who was he? How could he not remember? His hands clasped together tightly start to shake "It's alright because I do" Ava says

"What's my name?" he asks Ava, she seems to have answers that he needs.

"Thomas" Ava says and it fits it feels so right but wrong at the same time but if Ava says that's his name then his name it shall be after all he couldn't remember even if it wasn't.

"Thomas" he repeats and nods as Ava smiles widely at him "My name is Thomas"

 **So I am going to follow a bit in the past and present changing chapters, the next chapter is going to be about the present. Hope you enjoyed.**


	3. Chapter 3

**Chapter 3 Present time Thomas**

 **Well here is another chapter before I have to go back to college but I am really enjoying writing this, thanks for all the favs and follows. The next chapter after will go back to when Stiles first went missing.**

Thomas and Agent Penne had been in the interrogation room for a couple of hours now. It had gone a lot like this, Agent Penne asking questions he already knew answers for and Thomas giving the barest of details on it. As the minutes dragged into hours Thomas opened up more and more as time went on knowing he didn't have to answer if he didn't feel comfortable the hardest parts was answering questions on Chuck and Teresa, he had forgiven her after a week in the facility knowing they were all tricked and they had only given her memories of her time with Wicked, they were all doing what they believed to be right even if it was wrong.

"So I understand that the flare virus was not only effective on humans but also on sub-species as well" Agent Penne said not looking up from his tablet. "Thomas" He said raising his eyebrow and looking him in the eye.

"W-what do you mean? That's crazy there is no such thing" Thomas answered fear flashing through his body as he stammered before becoming more confident.

"Not even werewolves after all you did spend a time fighting feral ones infected by the flare" Red eyes flashed across his vision as a memory flashed up freezing him in his chair, he assessed the Agent in front of him after all they had been tricked before. Agent Penne did not seem to realise or care that Thomas was becoming closed up again as he carried on. "I know there was a certain women amongst you who told you not to mention anything about them to the government or they would think you were crazy, however we would not be a very decent government if we did not know of an entire different species or different supernatural creatures settling down with us."

"How? She said that they had hunters that hunted them and we had to be careful who we spoke" Thomas replied warily. Agent Penne smiled wrinkles appearing making him look much less scary than before as he let out a booming laugh that made Thomas just want to laugh a little with him, not that he did as he still felt wary around him.

"Who do you think sends out hunters well most, some live by their own code and we can't exactly lock them up, what with most people not believing that the supernatural is real" he winked and stood up before carefully putting his tablet away and collecting all his papers. "Thomas you can go and see your friends now" Thomas stood up and Agent Penne put a comforting hand on his shoulder but Thomas flinched away "you are not a prisoner but we have to do tests in order to figure out what has been done to you, we have some information but a lot was deleted before we got there but thank you for your co-operation it has been most helpful" Thomas nodded at the agent again before he headed out the door following a guard that would take him towards his friends.

 **Line Break Line Break Line Break Line Break Line Break Line Break**

Thomas followed the guard who mumbled something under his breath before stopping and nodding at the door giving a grunt when he stood there staring at the two doors. Thoughts swirled around Thomas head making him dizzy. Would they blame him? Would they still like him? What if they had found new friends? The guard finally having enough with the indecisiveness pulled open the door and shoved him inside before he even had a chance to take a breath, closing it behind him leaving him in the room. The first thing Thomas noticed was the horrid shade of wallpaper and he had seen some horrible stuff but the mouldy green of the room had just scarred him for life, well scarred him more.

"Have you had enough time eyeing up the wallpaper Tommy? or would you like to greet the quite less gross looking thing in the room?" Came a British voice behind him. Thomas spun around and was yanked into a crushing hug, he pulled away to see Newt standing there smiling at him.

"We wondered when you shank would turn up" Said a slightly deeper voice from behind Newt and outstepped Minho with a smaller grin on his face than Newt but looked just as pleased to see him. All the worry seemed to seep out of him at that moment as he grasped Minho and pulled him into a man hug, pulling away and laughing from the sheer joy of seeing them.

"I am so glad to see the both of you" Thomas said as he took them in they both looked much healthier. Newt was no longer as sickly pale looking and Minho seemed to be putting some muscle back on his body after months out in a desert with little or no food.

"I would have saved you more food but Min seems to have eaten most of it" Newt said in a teasing tone as he pulled Thomas to some thankfully normal and non-horrid looking coloured white table and chairs. Which had some food that seemed to be half missing; at least Minho looked a little apologetic.

"I am a growing man" Minho said as Thomas sat down opposite them.

"Yeah growing is one way to put it" Newt laughed as Minho threw a grape at him, which failed as Newt caught it in his mouth crunching down on it spraying juice everywhere.

"Hey save some for me, I am starving" Thomas said as he grabbed a plate and stuffed it with every kind of food he could.

"So…. I bet you have spoken to Agent Penne" Thomas nodded as Newt carried on "He seems like an alright guy much more honest well apart from bribing both of us with cakes."

"They were good cakes much better than we could ever get you know bef0re" Minho said flailing his hands about a bit.

"Chocolate cake was the best, Tommy you have never tasted something that truly reminded me of heaven" he laughed as Newt seemed to start dibbling.

"You seem to have a little something by your mouth" Thomas said mouth half full and trying not to spit his food out as Newt rubbed his hand across his mouth blushing a bit after being caught fanaticising about the chocolate cake. Minho laughed and chucked another grape which hit smack bang in the middle of his forehead at which Newt then glared half-heartedly at Minho before joining in the laughter. It reminded him of the first night in the maze where they had spent drinking and being so care free.

He must have said that out loud as Newt began to speak "You know what happened in the maze and after was not your fault; you tried to warn them, things happen Tommy"

"I just feel if though if I had never turned up in the maze nobody would have died"

"That's bullshit" They both looked at Minho then who shrugged "Well it is"

"He's right Tommy if you had not come we would be strung up and being harvested for a temporary cure, you saved us and if it wasn't for you I wouldn't be here right now" They all shivered at that thought "But we are safe. What we did managed to do for them not only to find us but to save a few others as well. What you did should have been impossible we had been running that maze for years and you where there months and you figured it out, there was always something about you the others were too blind in there ways to see it."

It was silent a while as they all contemplated what Newt had said but Thomas had felt better already, the guilt still clung to him but he didn't feel as heavy with it as before, he felt lighter now.

Minho lowered his voice to a slight whisper "I overhead a guard talking earlier he said that they are trying to track down our families well any we have left"

"Do you think there are any families out there looking for us?" Newt asked.

"Yeah" Thomas said certain "If not we will convince them to let us stick together after all family stays together through thick or thin"

"We have certainly been through thick." Minho said laughing as they all joined in and shared the good and bad memories.

 **Line Break Line Break Line Break Line Break**

At the same time in California in a town called Beacon Hills a house received a call and a man picked it up.

"Hello we are looking for Sheriff Stilinski" A male voice said

"That's me" said the Sheriff looking worn out with dark rings under his eyes and messed up hair after a long night on patrol. Without Stiles to look after him the sheriff had aged a decade in a few short years, his heart had been broken too much for him to handle much more sadness and after his son and his only reminder of Claudia, Sheriff Stilinski was a shattered man.

"This is the FBI"

"What business do you want from me?" There was only two things the FBI would want and they were both bad. He had worked with the FBI for a while after Stiles disappeared but as there was no proof he had been taken and large sums of money had disappeared from his bank account they had called Stiles a runaway and all hope of them helping find him was lost. The Sheriffs heart skipped a beat and panic overwhelmed him as he thought of Stiles body being found.

"We have found your son, Stiles Stilinski he's alive" The Sheriff let put a breath he had been holding as tears filled his eyes and his shattered heart started mending for the first time in years.

"Can I speak to him" The Sheriff asked his voice shaking a little at the anticipation of seeing and hearing his son again.

"Because of the delicate situation we feel that its best if we spoke to you in person before you spoke to him, I need to remind you Sheriff to keep this quiet and not to tell anyone else as this is a very delicate operation." The men carried on talking for another ten minutes then the sheriff put the phone down and let out a sob of joy, before rushing upstairs to pack.


	4. Chapter 4

**Chapter 4**

 **Ok so I know this is not like the books and films but just imagine some boys have been put in the maze already also in this chapter at the start is a bit more violent. I made some minor changes to the last chapter just at the end, Thank you Kage-ryu14 I rushed and I realised when you said about it the emotion in the last chapter there should be a little bit more. Thanks for everyone else for reviewing and the follows and favourites. Next chapter should be a bit more interesting and the chapter after that will be the last one in the past.**

 **2 days after Stiles went missing**

"Has he woken up yet" was the first thing Scott said as he walked into the basement. Derek was sat in the corner reading a book he raised an eyebrow and looked over at Scott. The worry since Stiles had gone had tripled in the days after especially since their only lead had not woken up.

"Why do you think I called?" Derek whilst standing up "It was only for a moment and he seemed more normal" Derek was checking to make sure the chains where secure when the chained up werewolf let out a whimper of pain. They both tensed and looked at him stepping back a bit to make sure that if he lashed out they would not get caught with his claws.

"He looks young" Scott whispered, Derek raised an eyebrow at him "Well younger than most"

"He is probably older than you are by a couple of years" The werewolf whimpered on the floor again but this time his eyes snap open and he jerks upright. His breathing and heart rate erratic as his no longer golden eyes sweep the room, he seemed terrified.

"Hey it's alright we are not going to hurt you, right Derek?" Scott said as though speaking to a baby, Derek rolled his eyes and nodded. The werewolf's gaze seemed to finally focus on them and calming down a little as the scent and panic and fear radiating from him disappeared a bit.

"Please kill me it hurts, please" He pleaded with Scott and Derek.

"It's alright I won't hurt you I promise, what's your name" Scott tries again.

"Subject 221" he mumbled quietly the panic fading even more as he relaxed.

"Subject 221?" Derek said more to himself than anyone else. Subject 221 nodded as he huddled into himself.

"You will make me better won't you, make the pain go away" Subject 221 said again.

"What do you mean?" Asked Derek a bit more curious.

"The people in white make everything better, make the pain go away" Derek and Scott shared a worried look between them.

"Who are the people in white?"

"Wicked" He whispered so quietly, as his eyes started to glow gold again his fangs descended and his claws came out "Wicked is good" he shouted as he plunged his claws into his chest, blood and flesh giving away under the sharp claws. Scott and Derek both jumped forward to restrain Subject 221 but the damage was done a feral grin etched onto his face as eyes blank stared up at him. Scott suddenly felt ill their only lead to his best friend gone and all they had was a place called wicked, if he hadn't faced what he has done, he would be on the floor sobbing his heart out but as an Alpha he had to stay strong especially for the rest of the pack.

 **Line Break Line Break Line Break**

Lydia sat at the library at school searching through a sea of books, there was nothing on this Wicked she had tried google to no avail, and it was frustrating her she could do maths equations in seconds but finding this stupid organisation had taken too long. She twisted a strawberry blond hair round her finger as she slammed another book shut, the librarian sent a glare her way before going back to her computer.

What would Stiles do in this situation probably look through every single google website, but Stiles was not here and so it was left up to her to pick up the clues. Clues? What clue "Wicked is good" If that was what she had then she would need an expert. She pulled out her phone and scrolled through the contacts till she had found who she was looking for and waited for him to pick up.

"Hello?" a male voice answered the phone.

"Hi Danny I need your help with something" he sighed on the other end of the phone.

"Ok what is it?"

"Can you find an organisation called Wicked" she heard typing before he answered again.

"Give me an hour and I will call you back" then he hung up. Lydia got up from the table and collected her things before she gave a smug smile to herself. If she didn't have the resources then she would find someone who did. She would help find Stiles in every way she knew how, she was half way to Derek's loft when her phone rang again. Pulling over she answered it.

"Hi"

"Right I found something but it not much, whatever it is they keep it locked down but I talked to some of the people who I know who do this sort of thing a lot. One was able to break through a layer of firewall once. Wicked stands for World in Catastrophe Killzone Department."

"But what do they do?" Lydia asked whatever it was it didn't sound good.

"Nobody is really sure but there seems to be some kind of lab connected with them, but that's all I can give you and even the best hackers can't get into their systems whoever they are they are bad news so stay away."

"Thanks Danny, I owe you"

"It doesn't matter as long as you don't call me for a while; it was nice speaking to you Lydia"

"You too Danny and thanks again" She hung up this time. They had gotten further than they had in a long time but if Stiles was with them it was bad news and nobody knew what they did and where they were. One step forward two steps back she thought as worry clenched her stomach, if they couldn't find Stiles what would happen to him. She had been holding off the rising panic for a while now but finding out a little bit about Wicked seemed to bring it all into perspective, she couldn't breath and think, all she could hope for was that Stiles was going to be alright.

 **Line Break Line Break Line Break**

Thomas had settled into the facility well, making friends with people like Chuck, Newt, Minho and Teresa. Teresa, Chuck and he had been fast friends straight away but Newt and Minho didn't like outsiders much and he was just that, but after a week and two missing puddings later they finally warmed up to him. It had been two weeks now and he had settled into a routine, every day they had testing some days it would be looking at equations others it would be solving impossible problems, Thomas enjoyed each and every one as they pushed him to want to achieve more.

"Hey Thomas I heard they have gotten you in for a late testing today." Minho said as he sat his tray down on the table next to him.

"Yeah something to do with that problem we had earlier apparently they want me to try it again" he replied.

"That sucks. Newt come sit here" Minho called out when he spotted Newt.

"Where are Teresa and Chuck?" Newt said as he sat down on the opposite side of the table.

"They still have testing" Thomas said.

"Aw poor them I just out of mine. Did you hear they are doing that choosing thing today" said Newt as he stuffed some food in his mouth.

"Wait what's this?" Thomas asked his curiosity spiking.

"Well once a month an individual is chosen to carry on their training, however once chosen we never see them again." Minho said lowering his voice so the guards couldn't over hear them as they didn't like them talking about it.

"Well this got morbid." Newt said laughing nervously "Any who speaking of, don't you need to head to your testing now."

"Aw man, I am going to be so late I will see you guys later." Thomas said as he sprinted off.

Thomas's testing had finished late and as he squeezed into the crowded room he saw Teresa just off to the side. He managed to reach her without too much trouble and sighed in relief when he could actually breath in the room.

"Hey" he whispered into her ear. She jumped and shot him a glare then smiling when she realised who it was.

"Did you see the others as I couldn't find them before" Teresa said to them.

"No I just got in here." he was about to speak again when a someone started speaking.

"Hello everyone." Ava said as she looked over the crowd briefly meeting Thomas's eyes. "Today we pick one lucky individual to progress forward. Those of you that have been here for a long time know what a great opportunity this is" she smiled as she looked at the piece of paper. "And the lucky one is" she waited as quite descended "Newton" Thomas's heart stopped as he saw a boy with blond hair stepped forward. Panic pulled at Thomas's heart as he started pushing through people trying to get to Newt. Just as he was going to grab hold of Newt he was pulled back by two guards further away from Newt. Newt was then escorted out another door and away from Thomas's sight.

"But I did even get to say goodbye" He whispered to himself as he was dragged out another door and into Avas office. Ava stormed in furious and slamming the door behind her as she sat down into her chair.

"You can go" she said to the guards but her eyes never leaving Thomas's who was started feeling nervous as his hands anxiously tapped his leg. "What do you think you are doing" Her voice dangerously calm. Thomas opened his mouth before he was cut off "however I do believe you can help me with something" she tapped something on her desk and then a screen was shown with peoples profiles "This is the maze trials and I want you to be a part of it" she tapped the screen again and then there was a video showing boys working in a field surrounded by large walls and some crude building put in place.

"What even is this place?" Thomas asked no longer nervous but curious.

"They call it the glade, a place where people go after they get chosen" Thomas looked at her suddenly comprehension dawning on him.

"Then that's where Newts going?"

"Yes"

"What will happen to him?" she smiled at him then.

"That's up to what you choose to do Thomas, if you work with us you can protect them and him"

"What happens if I don't?" she tapped the screen again and a giant black alien looking thing appeared on screen its beady eyes boring into him.

"Or we send these in, the choice is yours. After all we are all looking for a cure and it's for the good of the world" she looked at him waiting for his decision, he felt the weight of what was expected pressing down on him, but he couldn't let his friends die especially if he could prevent it, there was always only one decision that he would ever choose.

"Yes I will work with you" He managed to get out. Ava stood up smiling sincerely her white clothes portraying goodness where there was none.

"Just remember Thomas, Wicked is good" she smiled at him again before walking out.

"Wicked is good?" he heard himself repeat, fury bubbled inside him all he ever wanted was for his friends to be safe and now one was in trouble. He felt his hand curl up into a fist and punched the table revelling in the pain, at least it made him feel human. He let the anger that he felt towards Ava build and simmer under his skin he would get them out even if it meant he would had to go in. Clutching his aching hand he walked out of Avas office he would try to save them all.


	5. Chapter 5

**Chapter 5** **So its taken a long time to write this (because I am such a procrastinator seriously I am meant to be doing coursework) but I have a lot planned for this story so hopefully will continue writing it. Thanks for all the favourites, follows and reviews.**

Sheriff Stilinski pulled up into the field that the Agent had sent him directions for, it was surrounded by pine trees, long grass and wild flowers the perfect paradise. The Sheriff had a nervous energy surrounding him and it had been a day since the phone call. He was meant to meet an Agent here however here was in the middle of nowhere some miles from the nearest town. He was concerned that he had the wrong place and downright terrified that he might never get to see his son again. A noise descended across the no longer silent clearing as the trees swayed in the wind, the sheriff looked across the clearing to where the noise originated from to see a black military style helicopter heading towards him. The sheriff put his hands up to stop the wind buffeting him in the face as the helicopter landed in the clearing. A man jumped out his black coat flying in the wind that the helicopter still created, his greying black hair swept back slightly and his bright blue eyes sweeping over the sheriff.

"Agent Penne with the FBI, and you must be the sheriff" the Agent said holding out his hand to shake the sheriff shook back the man had a firm grip.

"Right I thought I was driving to the place" The Sheriff said he looked round as another agent got out of the helicopter and approached them.

"No heat signatures apart from ours and a couple of animals." The other Agent said looking at the contraption in his hands. "We are ready for take-off whenever you are sir"

"So you brought me out here, to what? Double check that I would risk telling anyone. I want to see my son more than anything." The Sheriff said angrily.

"Sorry about that Sheriff we had to bring you out here to pick you up, but we had to make sure after all. Where we are going is confidential, surly you can understand that?" Agent Penne said calmly shooting the other man a glare before carrying on "If you follow me we will take you to see your son now."

The Sheriff turned around to his car getting his bags out. "What about the car? Someone might think I am missing and start asking questions." Agent Penne thought for a moment before nodding at the other Agent to come closer.

"Drive the cruiser back to the station and tell the police that the Sheriff is looking at a special case for us, you can be back at the base tomorrow."

"Sir" The other Agent said angrily throwing his hand out for the keys, before getting into the car and driving off.

"He seems lovely" The Sheriff said sarcastically.

"We don't keep him around for his personality, he had certain skill sets" "I bet he has" the Sheriff muttered under his breath.

"Now if you would follow me, we really need to get back to base and brief you before seeing your son tomorrow."

They both headed to the chopper where the blades where starting to spin getting ready for take-off. Pulling himself up into the chopper he strapped himself in as Agent Penne settled opposite him. Nerves where setting in as the chopper took off he was going to see his son after all this time. Agent Penne smiled at him probably noticing his nerves as he schooled his face and just nodded back, after all he felt excitement and joy more than anything but still butterflies gripped his stomach making him feel sick, well that or the helicopter ride.

It was dark when they reached the base he couldn't see more than a white building surrounded by trees and situated on a cliff edge. It had taken at least a couple of hours to get here and he had dosed off for a little of it. Agent Penne jumped out motioning for him to follow, the wind whipped wildly in front of his face and his thin jacket didn't offer him much warmth from the icy wind. Someone had already taken out his stuff and he quickly followed Agent Penne into the warmth.

"Your son is in recovery room three at the moment" Agent Penne started "

Although I know you want to see him, he is sleeping and we need to speak to you before then."

"You keep mentioning that something happened, I have been a cop long enough to know you are not telling me something. Now what has happened with my son!" The Sheriff had become increasingly agitated especially since they had not giving him a straight answer.

"Sheriff I know it's been stressful especially the past few years, but I can't brief you right now. However tomorrow morning I will tell you all that we know happened to your son. Just trust us that he is safe and we will do everything to help him" Agent Penne said sincerely knowing how hard it was losing your family and not knowing what had happened. "Right let's get you to bed."

The sheriff went to bed that night with more worry than he had felt in year and by the time he went to sleep it was already the early hours of the morning.

The Sheriff had awoken from a fitful sleep managing somehow to fall asleep in the early hours of the morning. Rubbing the sleep out of his eyes he managed to stumble blearily to the bathroom half asleep still. Looking in the mirror he looked terrible with dark circles under his eyes and a spattering of stubble on his unshaven morning face, he hoped Stiles wouldn't panic too much at what he looked like. Stumbling through the rest of his morning routine he felt a lot better and had just managed to finish getting dressed when a knock sounded at his door.

"Come in" he called out. The door opened and a young man stepped in with a shortish brown hair that sort of reminded him of Stiles.

"Agent Penne is ready to debrief you Sir, whenever you're ready we will head down." The Agent said with a slightly deeper voice than expected. "Whenever your ready son and I didn't catch your name" he said looking him in his green eyes.

"That's because I didn't say Sir" he scratched his head as if considering if he was allowed to say "But its Jordan Parrish but everyone calls me Parrish, if you could follow me." Parrish said before heading out the door.

They travelled amongst the twisting corridors and up several flights of stairs, the nervousness of the night before had set in around the time they stepped out the room he was staying in. He wasn't nervous to meet his son but he had heard about and seen kidnapping victims some were the same some were traumatised. He just hoped to god that Stiles was healthy. They finally came to a stop in front of some steel doors.

"Here you are Sir, and I hope everything goes well" Parrish said before opening the door where Agent Penne sat.

"Come in" Agent Penne said "Sorry about the mess" he gestured to the table where half a dozen files where laid about "I haven't gotten round to organising it" The Sheriff sat down in the chair offered to him on the other side of the metal table.

"Been a while since I have been on the other side of one of these" he said jokily, Agent Penne let out a short bark of laughter.

"Right I know your anxious but we have a few things to cover first, before we start I have to tell you we don't know all that went on many of the records were lost however we have got an idea of what happened."

"To my son? What happened to him"

"We cannot tell you everything bu-"the sheriff slammed his hand on the table angrily.

"As a father and a Sheriff don't I get all the information; I have been out of my mind with worry for the past two years I am entitled to all the information you can give me!" he snapped at the man, he had waited two years and they couldn't get more information for him. Agent Penne took a deep breath

"How to put this lightly, your son has had his memories repressed he can't remember what it was like before where he was." All the fight drained out of the Sheriff and he started feeling sick.

"H-how is that possible"

"We are not a hundred percent certain the science behind it as it is experimental for us, at least, however we hope him being in a similar environment is going to bring some memories back. You have to be patient Sheriff he is very much afraid he has been through hell and back quite literally."

Agent Penne opened up a file and pulled out some pictures laying them out, they were all clearly Stiles but he was different his whisky coloured eyes held more wisdom, his brown hair shorter but not shaven and he was wearing a long sleeved t-shirt rather than his plaid shirt tops it was strange. But the shot of joy that his son was ok and that they had pictures was amazing and his heart leapt at the thought he would be seeing him.

"Right we have a lot to get through and little time before they bring your son up" And so the story began how they were used as an experiment, him put in a maze designed to train them, he believed his name was Thomas, they escaped, only to be caught again, then escape into a desert where they survived however Agent Penne wasn't allowed to say more than that but a little bit of information was all he wanted.

Thomas had been a nervous wreck all day his nervous energy flying all around the place, he felt so out of place. Thomas sat up on his bed trying to steady his breathing that had been rapidly getting sharper like he couldn't take in a deep breath. Thomas was about to run his hand through his hair when he realised his hands were shaking and with his breathing becoming shallower he had an overwhelming desire to just curl up into a ball. The more he thought about meeting this man no his father the more he panicked and the harder it got to breath until he felt his lungs burning and vision getting black spots around the edge. Through the mist of the attack Thomas has somehow pulled his emergency alarm and people were beginning to swarm him until an older lady with greying blond hair and bright blue eyes told everyone to get out.

"Thomas I need you to concentrate on me" she said calmly "Can you do that?"

"Y-yes" he said somewhat shakily through his gasping breaths.

"I need you to breath with me. Ready" he nodded starting to feel very dizzy "Breath in" she said taking a deep breath as Thomas followed as readily as he could "and out" they both let out a breath "And in" and he followed again finding it easier this time. They followed this pattern a few more times until Newt and Minho rushed into the room. He realised then that he was sitting on the floor with no idea how he had gotten there in all his panic.

"What was that" he rasped. "We call them a panic attacks, I am surprised you haven't had one before especially since all the stress and panic you've been through."

"You're alright through Tommy" Newt asked his and Minho expressions worried.

"Y-yeah I think so" he said truthfully.

"Good because you shuck gave us quite the scare with all those people rushing in and out" Minho said as the helped him to his feet. Thomas laughed a little at that.

"I always did love a bit of drama Min"

"Right you two out, shoo he needs some rest and peace while we check him over" The old nurse said.

"Yes Ma'am" Minho said rolling his eyes as Newt stuck his tongue out behind her back making Thomas laugh. "Right that's it, get out" she said shooing them out the door and closing it behind them. "Now" she said soothingly at him whilst getting him into bed "Panic attacks are caused by stress; you know if you don't want to meet your father you don't have to"

"No I do" he blurted out quickly before they changed their minds "it just that I was worried he wouldn't love you." She gave him a soft look taking his hand making him supress a flinch as the sudden contact.

"Oh sweetie, you know he will love you no matter what you are his son no matter who you are and you will always will be." She said softly "Now you are going back to bed" she said sternly "But what if"

"We will get you up in time and if you have any more worry's you can talk to us. All of you" she said raising her voice and opening the door where Newt and Minho tumbled in with guilty expressions.

"Now you two can keep him company for a while" she said whilst striding out of the room.

"I like her" Newt said bringing a chair up next to his bed "and if your father does not love you then he does not deserve you, but you still have us" Minho nodding. "Now where were we?" Minho asked.

"The properties of excellent food now we are no longer living in a desert" Thomas replied as Newt and him shared a glance and laughed as Minho talked about the food here until a couple of hours later when an Agent came to collect him.

"Time to go Thomas." The Agent said.

"Good luck, and if he doesn't like you we wil-"Newt began

"Have words with him" Minho cut in as Newt elbowed him. "Ouch" Minho shouted whilst rubbing his side.

Thomas smiled as he was led out of the room and into the corridors and by the time he walked into the empty room he felt a lot better. He had got to the point where counting the grey stones was fun when the door opened and Agent Penne came in followed by an older man more or less the same height as him, greying hair and blue eyes. He moved more into the room his hands twitching as though he wanted to grab him.

"Hey Kiddo" he said his face relaxing as he took all of him in "I missed you."


	6. Chapter 6

**Chapter 6**

 **Warning- It has a self-harm aspect in this chapter, but only for a short while.**

 **Thank you for all the support with favourites and follows, especially those who leave reviews. I am an extremely slow writer so it takes forever to get one chapter done.** **J**

The first thing the Sheriff noticed about Stiles was how tired he looked, the second was the untrusting gaze in his whisky coloured eyes.

When Agent Penne told the Sheriff that Stiles remembered nothing he never truly believed him, but Stiles looking at him, with no recognition that it was his father standing before him. It cut him deeper than he would like.

As the Sheriff sat down in the chair opposite he noted the change in Stiles appearance, his hair was cut shorter than he last saw it, falling flat on his forehead making him look older. He also filled out clothes more and held himself straighter and with more confidence.

He was no longer a gangly boy, but was now a man, the Sheriff had missed his little boy growing up.

Agent Penne sat in a chair beside Stiles, in which Stiles unconsciously moved away from him.

"Thomas, I would like you to meet your father" Agent Penne said, breaking the staring contest that the two men had started. "I know you two have a lot to talk about, but for security and confidential reasons I have to stay in here"

"It's because you don't trust me" Stiles spoke; his voice had not changed apart from but the depth and wisdom behind it had.

"Only because you don't trust us, and I understand why" Agent Penne winked, before moving the chair closer.

Stiles smiled slightly before turning to look back at him.

"Why don't you ask him some questions Sheriff." The Sheriffs brain went blank at that, what could he say. He had so many questions but no idea how to ask them.

"How are you? Have they treated you well?" the Sheriff asked, firing off questions to Stiles not really expecting an answer.

"Fine, and better than the last place" answering them "Are you really my father?" That shocked the Sheriff, Stiles had never really been that blunt before.

"Thomas, that was inappropriate" Chided Agent Penne, Thomas shrugged apologetically before looking back at the Sheriff.

"Look I trust that you know who I was, but I want proof. We have been tricked and betrayed too many times" The Sheriff had no clue what Stiles had been through, the once trusting kid was looking at him with suspicion.

The Sheriff nodded and reached down for his wallet, making Stiles tense up.

"I am just getting some pictures out" the Sheriff said softly. After Stiles had gone missing he had kept a few pictures in his pocket so that Stiles would never be far away.

He brought out his wallet, pulling the pictures out. Stiles reached out with trembling fingers and picked them up.

The first picture was Stiles barely five years old, he had been playing underneath an apple tree with Claudia. They were both smiling at the camera, matching whiskey eyes and grins.

"Who is she" Stiles asked, startling him out of his memories.

"She was your mother; you were only five when that was taken" Stiles touched Claudia's face.

"Was?" Stiles asked in a small voice, so like Stiles when he had first lost his mother.

"Stiles, she died when you were only eight" It still confused him that Stiles had no memories, not even the ones of the people that he loved the most.

"Was that my name?" The Sheriffs heart gave a jolt, he shouldn't have been surprised that Stiles didn't remember his name, but he had hoped deep down that he would.

"No it was only a nickname, your real name was unpronounceable to anyone other than Claudia" He remembered when Claudia used to whisper it to Stiles, she always laughed when no one else could pronounce it, said it was their little secret.

"Could you call me Thomas" Stiles said softly "I know I am Stiles, but Thomas is the only name I have ever known." Stiles picked up the pictures again, touching Claudia's face again.

"Ok" The Sheriff conceded as Stiles moved onto the next picture.

This one was Stiles and him at an annual police ball. Stiles had chocolate all over his shirt from where he had been eating from the chocolate fountain, later that night he threw up from eating too much. The final picture was taken a year before Stiles had been taken, they were standing in front of his jeep. It was an early birthday present and they were both smiling and laughing as Scott took the picture.

"Dad?" Stiles looks at him. The tears that had threatened to fall earlier slid down his face, as he choked back a sob.

As his dad broke down sobbing, Thomas didn't know what to do, he didn't know what he had said to make his Dad brake down.

"Give him a hug" Agent Penne whispered in his ear.

Thomas lent over the table, pulling his father into his arms. His father gripped him back, it was only a couple of moments till his Dad pulled back.

"Sorry, Sti-Thomas it's just been so long since I heard you say that" His Dad said as he dried his face onf the back of his hand.

"That's ok, I didn't even know I had a family" Thomas knew he had a family once, but to him they had been gone for a long time. It would be weird to have a family outside of the maze.

"Do you want to be a family again? Go to school and have a normal life" His Dad sounded so hopeful, Thomas didn't want to say no, but he didn't think he would ever be what his father wanted.

"I don't know if I would ever have a normal life, I would like however to try and be a family" Thomas truly smiled at his Dad. Thomas may not remember his Dad, but he felt as though he loved him.

"You can come home whenever you want, I would love to have you back. I left your room how it was when, you know…." The sheriff said expectantly. Hands held out towards him welcoming him home.

Before Thomas was able to answer the door opened, a looming figure walked in.

One moment Thomas was sitting down, before his hand had reached for Agent Penne's gun and was aiming it at the intruder. He came back to himself with shouting all around him and Agent Penne aiming a gun at him.

"Thomas drop the gun" Agent Penne shouted at him. Thomas looked around the room, his Dads pale face and shocked expression overwhelmed him.

Thomas dropped the gun before collapsing to the floor himself, he was shaking and tears were running down his face. Agent Penne moved the gun away from Thomas, before coming to check on him.

The next ten minutes were a blur of people, rooms and places as they moved him through the facility. He ended back up in his room, where he was just left alone with his thoughts.

Thomas was angrier at himself than anything else, how could he let WICKED get to him like that. He had worked hard these past weeks, and then he had let it all slip. He had just reacted, he had thought that person was a threat. His father had seen; how would he look at his son now? He was a monster.

Thomas punched the wall, once he had started he couldn't stop. The pain and rhythm of it made him feel better.

"Thomas!" Someone yelled, grabbing his hand which had cuts and bruises forming across it. If he had been lucky it wouldn't be broken.

"Someone should have been watching you." The kindly old nurse tutted. Carefully she moved him across the room to sit down on the bed, she started getting out equipment to clean his wounds. Thomas clenched the bedding as she began to clean his wounds, the stinging overwhelming him for a moment.

"I-is the man I pointed the gun at okay" Thomas asked his voice small. He hoped he had not shot someone; these past weeks he had not had the best self-control.

"Jordan? He's been in far worse situations than that, he should have known to knock. He's okay sweetie, it's you we are worried about" Her voice soft and kind as she worked upon his hand.

Thomas flinched at that, they all thought he was broken then.

"Not like that. Thomas what you have been through was like a war zone, soldiers have problems adjusting back to civilian life. You are no different than anyone else from being through a trauma, it's just that we should have expected something like this." She had a slight frown on her face.

"Something like this?" Thomas asked confused.

"We call it PTSD, that stands for Post-Traumatic Stress Disorder. I bet even Newt and Minho have a milder form, what you did in there you did because you felt threatened." Thomas smiled at that, he always has been slightly impulsive, not thinking before he acted.

"Thank you. I feel since I came out of the box in the maze, everyone's expectations have been put on my shoulders." Thomas admitted, the nurse smiled at him before finishing up bandaging his hand.

"There you go dear. Promise me Thomas, that if you get frustrated or angry, you won't take it out on yourself. There are other ways to deal with it, we can help you that's why we are here." He would take her up on that offer, or would talk to Minho and Newt.

"I promise" She patted his arm, and headed towards the door.

"Agent Penne will be in to see you shortly, take care of yourself Thomas. I hope I won't be bandaging up your hand for a very long time." She walked out the door, she had made Thomas feel a whole lot better about the whole ordeal.

"WHAT THE HELL WAS THAT!" The Sheriff shouted. His son had just walked out of the room after aiming a gun at Jordan. To say he was shocked was an understatement, but honestly he was more worried about Stiles.

"We thought they may have a form of PTSD; what they have been through I can't even compare." Agent Penne sighed before leading the Sheriff out of the room and into another. "Stiles was not the only one found, there are others. Stiles he was chosen to be their leader, he even worked with WICKED for a while."

"Does that mean that many others were found?" The Sheriff asked shocked, he hadn't even thought of the other people that may have been involved.

"Too few" Agent Penne sounded sad, "We hadn't even connected the missing people case until a few months ago, unfortunately we were too late for many." Agent Penne, flipped a switch and the blacked glass turned slightly transparent. The Sheriff walked towards the glass, he didn't know what to expect but it wasn't two boys in a living room looking area. Two huge sofas were place in front of a high tech TV.

"They were with Stiles, we found them together." Agent Penne pointed to the blond, skinny boy stretched out on one of the sofas. "When we found Newt he was dying and Thomas was holding him, we had to drag them away from one another." He didn't look like much but he had a wiry strength much like Stiles had.

"We want to transfer them to a different place. But we really need parental permission" Agent Penne raised an eyebrow at the Sheriff.

"Why ask me? I am neither their father or family" The Sheriff said shocked, unless he had randomly had a few drunk one night stands it was highly unlikely.

"We want to move Stiles closer, not only can you go back to work but can visit Stiles as often as you like. Unfortunately for them we have not been able, to find any family as of yet, and Stiles would not leave without them" The Sheriff felt thrilled, he could have Stiles home and they could make up for lost time.

"Wait, visit?"

"Yes unfortunately, Stiles has been through a lot. We also want to make sure that he can settle back into a normal life and school." The Sheriff understood why, it didn't mean he had to like it.

"Newt and Minho need help too; they would settle back in a lot quicker together." Minho must be the other boy in the room, he was buffer than the other. He had a serious expression on his face as he listened to something that Newt was saying to him.

"If it helps my son settle in better, I will do it." The Sheriff accepted, these boys needed help too. They sounded like Stiles family and he would do anything for family.

"Great, we fly the boys out tomorrow." Agent Penne smiled, he flicked the switch and the glass went black again.

"Where is this new facility going to be?" he had only been told it was closer, didn't mean it could be over an hour's drive.

Agent Penne had a knowing expression on his face "Just outside Beacon Hills, welcome home Sheriff"


End file.
